The monastery was founded by Donna Maura Dias in 1280 for the nuns of Clarissa. The monastery did not last long, and in 1311 he ceased to exist. In 1316 year, the wife of king Dinis I, Queen Isabella Portuguese, restored the monastery.

The Queen Isabella Portuguese called "Holy Queen" because of her exceptional piety and righteousness. The Queen was also known for his good nature, founded hospitals, orphanages and schools. After the death of her husband, king Dinis, she retired to this monastery. And in 1336, the Queen died and was buried in the monastery in the tomb, decorated in the Gothic style. In 1626 Queen Isabella was canonized for his charity and good deeds.

The first architect of the monastery was Domingos Domingues, known for his work on the galleries of the monastery of Alcobaça. Continued the work of this architect, Estevao Dominguez, who was famous for his work on the galleries of the Cathedral in Lisbon. In 1330 the consecration of the temple, and later to the southern part of the Church was added to the monastery. The monastery is very often presented cash donations and gifts. In the early sixteenth century the Church was decorated with Sevillian tiles and installed new altars.

As far as the monastery and Church were built on the left Bank of the river Mondego, in the year of the building were flooded flooded waters of the river. And for several centuries the monastery has been flooded many times. Due to frequent floods in the monastery was impossible to stay, and king John IV ordered to leave the building and move to a new monastery - the monastery of Santa Clara-a-Nova, built on a hill near the old building. The tomb containing the ashes of Queen Isabel and other Royal persons was moved to the new building.

Over time, the old monastery in ruins. In 1910 the building was entered in the list of monuments of national importance, and some reconstruction works were carried out in the first half of the twentieth century.